Experimental and theoretical electron momentum spectroscopic study of the valence electronic structure of tetrahydrofuran under pseudorotation

The most populated structure of tetrahydrofuran (THF) has been investigated in our previous study using electron momentum spectroscopy (EMS). Because of the relatively low impact energy (600 eV) and low energy resolution (DeltaE = 1.20 eV) in the previous experiment, only the highest occupied molecular orbital (HOMO) of THF was investigated. The present study reports the most recent high-resolution EMS of THF in the valence space for the first time. The binding energy spectra of THF are measured at 1200 and 2400 eV plus the binding energies, respectively, for a series of azimuthal angles. The experimentally obtained binding energy spectra and orbital momentum distributions (MDs) are employed to study the orbital responses of the pseudorotation motion of THF. The outer valence Greens function (OVGF), the OVGF/6-311++G** model, and density function theory (DFT)-based SAOP/et-pVQZ model are employed to simulate the binding energy spectra. The orbital momentum distributions (MDs) are produced using the DFT-based B3LYP/aug-cc-pVTZ model, incorporating thermodynamic population analysis. Good agreement between theory and experiment is achieved. Orbital MDs of valence orbitals exhibit only slight differences with respect to the impact energies at 1200 and 2400 eV, indicating validation of the plane wave impulse approximation (PWIA). The present study has further discovered that the orbital MDs of the HOMO in the low-momentum region (p < 0.70 a.u) change significantly with the pseudorotation angle, phi, giving a v-shaped cross section, whereas the innermost valence orbital of THF does not vary with pseudorotation, revealing a very different bonding mechanism from the HOMO. The present study explores an innovative approach to study pseudorotation of sugar puckering, which sheds a light to study other biological systems with low energy barriers among ring-puckering conformations.     

Methylation of zebularine investigated using density functional theory calculations

Deoxyribonucleic acid (DNA) methylation is an epigenetic phenomenon, which adds methyl groups into DNA. This study reveals methylation of a nucleoside antibiotic drug 1‐(β‐D ‐ribofuranosyl)‐2‐pyrimidinone (zebularine or zeb) with respect to its methylated analog, 1‐(β‐D ‐ribofuranosyl)‐5‐methyl‐2‐pyrimidinone (d5) using density functional theory calculations in valence electronic space. Very similar infrared spectra suggest that zeb and d5 do not differ by types of the chemical bonds, but distinctly different Raman spectra of the nucleoside pair reveal that the impact caused by methylation of zeb can be significant. Further valence orbital‐based information details on valence electronic structural changes caused by methylation of zebularine. Frontier orbitals in momentum space and position space of the molecules respond differently to methylation. Based on the additional methyl electron density concentration in d5, orbitals affected by the methyl moiety are classified into primary and secondary contributors. Primary methyl contributions include MO8 (57a), MO18 (47a), and MO37 (28a) of d5, which concentrates on methyl and the base moieties, suggest certain connection to their Frontier orbitals. The primary and secondary methyl affected orbitals provide useful information on chemical bonding mechanism of the methylation in zebularine. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Density functional theory study of calix[4]arene‐N‐azacrown‐5, calix[4]arene‐N‐phenyl‐azacrown‐5, and their complexes with alkali‐metal cations: Na+, K+, and Rb+

Theoretical studies of 1,3‐alternate‐25,27‐bis(1‐methoxyethyl)calix[4]arene‐azacrown‐5 ( L₁ ), 1,3‐alternate‐25,27‐bis(1‐methoxyethyl)calix[4]arene‐N‐phenyl‐azacrown‐5 ( L₂ ), and the corresponding complexes M⁺/ L of L₁ and L₂ with the alkali‐metal cations: Na⁺, K⁺, and Rb⁺ have been performed using density functional theory (DFT) at B3LYP/6‐31G* level. The optimized geometric structures obtained from DFT calculations are used to perform natural bond orbital (NBO) analysis. The two main types of driving force metal–ligand and cation–π interactions are investigated. The results indicate that intermolecular electrostatic interactions are dominant and the electron‐donating oxygen offer lone pair electrons to the contacting RY* (1‐center Rydberg) or LP* (1‐center valence antibond lone pair) orbitals of M⁺ (Na⁺, K⁺, and Rb⁺). What's more, the cation–π interactions between the metal ion and π‐orbitals of the two rotated benzene rings play a minor role. For all the structures, the most pronounced changes in geometric parameters upon interaction are observed in the calix[4]arene molecule. In addition, an extra pendant phenyl group attached to nitrogen can promote metal complexation by 3D encapsulation greatly. In addition, the enthalpies of complexation reaction and hydrated cation exchange reaction had been studied by the calculated thermodynamic data. The calculated results of hydrated cation exchange reaction are in a good agreement with the experimental data for the complexes. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Remarkable Shape‐Sustaining,Load‐Bearing,and Self‐Healing Properties Displayed by a Supramolecular Gel Derived from a Bis‐pyridyl‐bis‐amide of L‐Phenyl Alanine

A series of bis‐amides decorated with pyridyl and phenyl moieties derived from L ‐amino acids having an innocent side chain (L ‐alanine and L ‐phenyl alanine) were synthesized as potential low‐molecular‐weight gelators (LMWGs). Both protic and aprotic solvents were found to be gelled by most of the bis‐amides with moderate to excellent gelation efficiency (minimum gelator concentration=0.32–4.0 wt. % and gel–sol dissociation temperature T_gel=52–110 °C). The gels were characterized by rheology, DSC, SEM, TEM, and temperature‐variable ¹H NMR measurements. pH‐dependent gelation studies revealed that the pyridyl moieties took part in gelation. Structure–property correlation was attempted using single‐crystal X‐ray and powder X‐ray diffraction data. Remarkably, one of the bis‐pyridyl bis‐amide gelators, namely 3,3‐Phe (3‐pyridyl bis‐amide of L ‐phenylalanine) displayed outstanding shape‐sustaining, load‐bearing, and self‐healing properties.     

Orbital signatures of methyl in L-alanine

Molecular orbital signatures of the methyl substituent in L-alanine have been identified with respect to those of glycine from information obtained in coordinate and momentum space, using dual space analysis. Electronic structural information in coordinate space is obtained using ab initio (MP2/TZVP) and density functional theory (B3LYP/TZVP) methods, from which the Dyson orbitals are simulated based on the plane wave impulse approximation into momentum space. In comparison to glycine, relaxation in geometry and valence orbitals in L-alanine is found as a result of the attachment of the methyl group. Five orbitals rather than four orbitals are identified as methyl signatures. That is, orbital 6a in the core shell, orbitals 11a and 12a in the inner valence shell, and orbitals 19a and 20a in the outer valence shell. In the inner valence shell, the attachment of methyl to glycine causes a splitting of its orbital 10a' into orbitals 11a and 12a of L-alanine, whereas in the outer valence shell the methyl group results in an insertion of an additional orbital pair of 19a and 20a. The frontier molecular orbitals, 24a and 23a, are found without any significant role in the methylation of glycine.     

饱和烷烃分子C_nH_(2n+2)(n=4-6)的电子动量光谱(英文)

使用B3LYP/TZVP//B3LYP/aug-cc-pVTZ方法系统研究了饱和烷烃分子CnH2n+2(n=4-6)的轨道电子动量光谱,比较了同分异构体CnH2n+2(n=4-6)对轨道动量分布的影响.结合二维空间分析方法对电子在坐标空间中的密度分布进行了系统的研究.计算结果表明,最内价壳层电荷分布主要由s电子贡献,第二近邻芯价壳层则主要由p电子贡献,而其余的价壳层则为sp杂化.最内价轨道表现出最大的谱线强度并且远大于其它轨道的谱线强度,而且正烷烃的谱线强度要大于异烷烃等同分异构体的谱线强度,表现出了明显的与甲基移动的个数有关的性质.     

Core molecular orbital contribution to N2O isomerization as studied using theoretical electron momentum spectroscopy

Core molecular orbital contribution to the electronic structure of N2O isomers has been studied using quantum mechanical density functional theory combined with a plane wave impulse approximation method. Momentum distributions of wave functions for inner shell molecular orbitals of the linear NNO, cyclic and linear NON isomers of N2O are calculated through the (e, 2e) differential cross sections in momentum space. This is possible because this momentum distribution is directly proportional to the modulus squared of the momentum space wave function for the molecular orbital in question. While the momentum distributions of the NNO and cyclic N2O isomers demonstrate strong atomic orbital characteristics in their core space, the outer core molecular orbitals of the linear NON isomer exhibit configuration interactions between them and the valence molecular orbitals. It is suggested that the frozen core approximation breaks down in the prediction of the electronic structure of such an isomer. Core molecular orbital contributions to the electronic structure can alter the order of total energies of the isomers and lead to incorrect conclusions of the stability among the isomers. As a result, full electron calculations should be employed in the study of N2O isomerization.     

Full spectral decomposition of ring currents

Within the ipsocentric method for calculation of molecular magnetic response, projection of perturbed orbitals onto the virtual orbital space allows partition of induced current density into contributions from individual virtual excitations between occupied and unoccupied orbitals, enabling detailed assignment of the origin of currents in, e.g., benzene, cyclooctatetraene, borazine, coronene, and corannulene. Whereas delocalized currents in benzene and planar cyclooctatetraene are described by transitions within the valence space, localized currents in the borazine pi system involve excitations outside the valence space.     

Localization of molecular orbitals on fragments

A non‐iterative algorithm for the localization of molecular orbitals (MOs) from complete active space self consistent field (CASSCF) and for single‐determinantal wave functions on predefined moieties is given. The localized fragment orbitals can be used to analyze chemical reactions between fragments and also the binding of fragments in the product molecule with a fragments‐in‐molecules approach by using a valence bond expansion of the CASSCF wave function. The algorithm is an example of the orthogonal Procrustes problem, which is a matrix optimization problem using the singular value decomposition. It is based on the similarity of the set of MOs for the moieties to the localized MOs of the molecule; the similarity is expressed by overlap matrices between the original fragment MOs and the localized MOs. For CASSCF wave functions, localization is done independently in the space of occupied orbitals and active orbitals, whereas, the space of virtual orbitals is mostly uninteresting. Localization of Hartree–Fock or Kohn–Sham density functional theory orbitals is not straightforward; rather, it needs careful consideration, because in this case some virtual orbitals are needed but the space of virtual orbitals depends on the basis sets used and causes considerable problems due to the diffuse character of most virtual orbitals. © 2012 Wiley Periodicals, Inc.     

Valence orbital response to pseudorotation of tetrahydrofuran: a snapshot using dual space analysis

The pseudorotation of tetrahydrofuran (THF) (C(4)H(8)O) has been studied using density functional theory, with respect to the valence orbital responses to the ionization potentials and to orbital electron and momentum distributions. Three conformations of THF, the global minimum structure C(s), local minimum structure C(2), and a transition state structure C(1), which are characteristic configurations on the potential energy surface, are examined using the SAOP/et-pVQZ//B3LYP/6-311++G** models with the aforementioned dual space analysis. It is noted in the ionization energy spectra that the minimum structures C(s) and C(2) are not directly connected by pseudorotation, but through the transition state structure C(1). As a result, some orbitals of the C(s) conformer are able to "correlate" to orbitals of the C(2) conformer without a strict symmetry constraint, i.e., orbital 7a' of the C(s) conformer is correlated to orbital 5b of the C(2) conformer. It is also noted that although the valence orbital ionization potentials are not significantly altered by the pseudorotation of THF, their spectra (mainly due to excitation) are quite different indeed. Detailed orbital analysis based on dual space analysis is given. The valence orbital behavior of the conformations is orbital dependent. It can be approximately divided into three groups: the "signature group" is associated with orbitals experiencing significant changes. The frontier orbitals are in this group. The "nearly identical group" includes orbitals without apparent changes across the conformations. Most of the orbitals showing a certain degree of distortion during the pseudorotation process belong to the third group. The present study demonstrates that a comprehensive understanding of the pseudorotation of THF and its dynamics requires multidimensional information and that the information gained from momentum space is complementary to that from the more familiar coordinate space.     

New Fluorescence Domain “Excited Multimer” Formed upon Photoexcitation of Continuously Stacked Diaroylmethanatoboron Difluoride Molecules with Fused π‐Orbitals in Crystals

The crystal‐packing structures of seven derivatives of diaroylmethanatoboron difluoride ( 1 a – gBF₂ ) are characterized by no overlap of the π‐conjugated main units of two adjacent molecules (type I), overlap of the benzene ring π‐orbitals of two adjacent molecules (type II), and overlap of the benzene and dihydrodioxaborinine rings π‐orbitals of adjacent molecules (type III). The crystal‐packing structures govern the fluorescence (FL) properties in the crystalline states. The FL domain that is present in type I crystals, in which intermolecular orbital interactions are absent, leads to excited monomer‐like FL properties. In the case of the type II crystals, the presence of intermolecular overlap of the benzene rings π‐orbitals generates new FL domains, referred to as “excited multimers”, which possess allowed S₀–S₁ electronic transitions and, as a result, similar FL lifetimes at longer wavelengths than the FL of the type I crystals. Finally, intermolecular overlap of the benzene and dihydrodioxaborinine ring π‐orbitals in the type III crystals leads to “excited multimer” domains with forbidden S₀–S₁ electronic transitions and longer FL lifetimes at similar wavelengths as that in type I crystals.     

Valence-shell momentum distributions and ionization energies of carbon disulfide

Valence-shell binding energy spectra and momentum distributions of CS₂ have been measured using non-coplanar symmetric binary (e,2e) spectroscopy. The present measurements are compared with previously published binding energy spectra calculated using the many body 2ph-TDA Green's function (GF) method and the symmetry-adapted cluster configuration-interaction (SAC CI) method. The measured and the calculated binding energy spectra both show extensive population splittings particularly above 20 eV, confirming a significant breakdown of independent particle ionization picture. A relatively strong-outer valence many-body state at 17.0 eV is shown to be satellite of the (2π₀)^?1 state, in accord with earlier conclusions of photoelectron studies. Momentum distributions measured at several carefully chosen binding energies are compared with the corresponding molecular orbital momentum distributions calculated using small and extended gaussian basis sets. The good qualitative agreement between momentum distributions measured in the inner-valence region wth theoretical 4σ_m and 5σ_g orbital momentum distributions confirms the qualitative predictions of satellite parentages by GF and SAC CI calculations. Momentum and position density contour maps of individual orbitals are used to interpret the shapes and atomic characters of the experimental momentum distributions. Momentum densities of the valence orbitals of CS₂ are compared with those of the respective valence isoelectronic species CO₂     

Coexistence of 1,3-butadiene conformers in ionization energies and Dyson orbitals

The minimum-energy structures on the torsional potential-energy surface of 1,3-butadiene have been studied quantum mechanically using a range of models including ab initio Hartree-Fock and second-order M?ller-Plesset theories, outer valence Green's function, and density-functional theory with a hybrid functional and statistical average orbital potential model in order to understand the binding-energy (ionization energy) spectra and orbital cross sections observed by experiments. The unique full geometry optimization process locates the s-trans-1,3-butadiene as the global minimum structure and the s-gauche-1,3-butadiene as the local minimum structure. The latter possesses the dihedral angle of the central carbon bond of 32.81 degrees in agreement with the range of 30 degrees-41 degrees obtained by other theoretical models. Ionization energies in the outer valence space of the conformer pair have been obtained using Hartree-Fock, outer valence Green's function, and density-functional (statistical average orbital potentials) models, respectively. The Hartree-Fock results indicate that electron correlation (and orbital relaxation) effects become more significant towards the inner shell. The spectroscopic pole strengths calculated in the Green's function model are in the range of 0.85-0.91, suggesting that the independent particle picture is a good approximation in the present study. The binding energies from the density-functional (statisticaly averaged orbital potential) model are in good agreement with photoelectron spectroscopy, and the simulated Dyson orbitals in momentum space approximated by the density-functional orbitals using plane-wave impulse approximation agree well with those from experimental electron momentum spectroscopy. The coexistence of the conformer pair under the experimental conditions is supported by the approximated experimental binding-energy spectra due to the split conformer orbital energies, as well as the orbital momentum distributions of the mixed conformer pair observed in the orbital cross sections of electron momentum spectroscopy.     

An investigation of valence shell orbital momentum profiles of difluoromethane by binary (e,2e) spectroscopy

The electron binding energy spectra and momentum profiles of the valence orbitals of difluoromethane, also known as HFC32 (HFC-hydrofluorocarbon) (CH(2)F(2)), have been studied by using a high resolution (e,2e) electron momentum spectrometer, at an impact energy of 1200 eV plus the binding energy, and by using symmetric noncoplanar kinematics. The experimental momentum profiles of the outer valence orbitals and 4a(1) inner valence orbital are compared with the theoretical momentum distributions calculated using Hartree-Fock and density functional theory (DFT) methods with various basis sets. In general, the shapes of the experimental momentum distributions are well described by both the Hartree-Fock and DFT calculations when large and diffuse basis sets are used. However, the result also shows that it is hard to choose the different calculations for some orbitals, including the methods and the size of the basis sets employed. The pole strength of the ionization peak from the 4a(1) inner valence orbital is estimated.     

Outer valence orbital momentum distributions of carbon dioxide by binary (e,2e) spectroscopy

The outer valence orbital momentum distributions of CO₂ have been reinvestigated using a high momentum resolution (0.1 a_o^?1 fwhm) binary (e,2e) spectrometer operated at 1200 eV impact energy under the non-coplanar symmetric scattering condition. Generally good agreement of the measured momentum distributions with theoretical momentum distributions calculated using literature SCF double-zeta quality wavefunctions has been obtained for the 1π_g, (1π_u + 3σ_u) and 4σ_g orbitals. Although there is a reasonable agreement of the measured momentum distributions with earlier low momentum resolution (0.4 a_o^?1 fwhm) non-coplanar measurements at 400 eV impact energy reported by Cook and Brion, given the large differences in the momentum resolutions much more definitive results are obtained in the present study. In particular, the significantly higher momentum resolution clearly shows the mixed s-p character of the 4σ_g orbital. The present study also gives a much better agreement with theory in the case of the 4σ_g momentum distribution. For each orbital the calculated and where possible the experimentally determined spherically averaged momentum distributions are compared and contrasted with their respective two-dimensional momentum and position density maps. These together with three-dimensional surface plots at selected constant density values of the four outermost orbitals are used to provide a detailed comparison of momentum-space bonding and orbital properties with their more familiar position-space counterparts in the CO₂ triatomic molecule. The calculated momentum-space density contour maps of the core orbitals exhibit rather large density oscillations and the feasibility of future experiments is discussed.     

Ab initio through‐space/bond interaction analysis of the long C–C bonds in Bi(anthracene‐9,10‐dimethylene) photoisomers

The bi(anthracene‐9,10‐dimethylene) photoisomer has remarkably long C–C single bonds. To examine the lengthening of the C–C bond, we propose a novel procedure for quantitatively analyzing orbital interactions in a molecule at the level of the ab initio molecular orbital method. In this procedure, we can cut off the specific through‐space/bond interactions in a molecule by artificially increasing the absolute magnitude of the exponents in a Gaussian function. Then, the spatial orbital interactions were perfectly cut off, and, each term that makes up the total energy, that is, the nuclear–electron attractions, the electron–electron repulsions, and the nuclear–nuclear repulsions cancel each other. Several model molecules of the photoisomer were analyzed by this procedure. It was found that the orbital interaction between the p orbital on the benzene ring and the σ* orbital on the C–C bond in question, σ→σ* electron transfer through π orbital, weakens the C–C bond efficiently when these orbitals were located in the “periplanar” conformation. © 2001 John Wiley & Sons, Inc. Int J Quantum Chem, 2001     

Investigation on thermoresponsive behavior of biodegradable poly(γ‐glutamic acid)‐graft‐L‐phenylalanine ethyl ester

The thermosensitivity of biodegradable and non‐toxic amphiphilic polymer derived from a naturally occurring polypeptide and a derivative of amino acid was first reported. The amphiphilic polymer consisted of poly(γ‐glutamic acid) (γ‐PGA) as a hydrophilic backbone, and L ‐phenylalanine ethyl ester (L ‐PAE) as a hydrophobic branch. Poly(γ‐glutamic acid)‐graft‐L ‐phenylalanine (γ‐PGA‐graft‐L ‐PAE) with grafting degrees of 7–49% were prepared by varying the content of a water‐soluble carbodiimide (WSC). γ‐PGA‐graft‐L ‐PAE with a grafting degree of 49% exhibited thermoresponsive phase transition behavior in an aqueous solution at around 80°C. The copolymers with grafting degrees in the range of 30–49% showed thermoresponsive properties in NaCl solution. A clouding temperature (T_cloud) could be adjusted by changing the polymer concentration and/or NaCl concentration. The thermoresponsive behavior was reversible. © 2012 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2012     

Valence electronic structure of CH3Br and CH3I: Electron momentum distributions and separation energies

Bromomethane (CH₃Br) and iodomethane (CH₃I) have been studied by binary (e,2e) coincidence spectroscopy at 1200 eV using non-coplanar symmetric kinematics. Separation energy spectra have been determined in the energy range up to 47 eV at azimuthal angles of 0° and 8° for CH₃Br and 0° and 6° for CH₃I. The separation energy spectra and the electron momentum distributions measured for each of the valence orbitals are compared with theoretical predictions employing SCF wavefunctions and outer valence type and extended 2 ph-TDA Green function calculations. Electron density and momentum density maps have been calculated for all the valence orbitals using the SCF wavefunctions, and they are used to explain trends and contrasts in the electronic structure and bonding properties of these halomethanes in both position and momentum space.     

The valence and Rydberg excited states of CH2: A theoretical exploration

Using the completed active space second‐order perturbation (CASPT2) method, valence and Rydberg excited states of CH₂ molecule are probed with the large atomic natural orbital (ANO‐L) basis set. Five states are optimized and the geometric parameters are in good agreement with the available data in literatures, furthermore, the state of 2¹B₁ is obtained for the first time. Valence and Rydberg excited states of CH₂ are also calculated for the vertical transitions with the ANO‐L+ basis set that is constructed by adding a set of 1s1p1d Rydberg orbitals into the ANO‐L basis set. Two Rydberg states of the p?³A₂ and r?³B₁ at 9.88 and 10.50 eV are obtained for the first time, and the 3a₁ → 3d_yz nature of the state p?³A₂ and the 3a₁ → d_x2?y2 nature of the state r?³B₁ are confirmed. © 2012 Wiley Periodicals, Inc.     

Mechanistic Investigation of Phenylalanine Ammonia Lyase by Using N‐Methylated Phenylalanines

N‐Methyl‐L ‐phenylalanine ( 5 ), N‐methyl‐4‐nitro‐L ‐phenylalanine ( 6 ), and N,N‐dimethyl‐4‐nitro‐L ‐phenylalanine ( 7 ?H⁺) were investigated as substrates or inhibitors of phenylalanine ammonia lyase from Petroselinum crispum. Whereas the former was a reluctant substrate (K_m =6.6 mM , k_cat =0.22 s^?1), no reverse reaction could be detected by using methylamine and (E)‐cinnamate ( 2 ). The K_m value for ammonia in the reverse reaction by using (E)‐cinnamate ( 2 ) was determined to be 4.4 and 2.6M at pH 8.8 and 10, respectively. The N‐methylated 4‐nitro‐L ‐phenylalanines 6 and 7 showed only strong inhibitory effects (K_i =130 nM and 8 nM , resp.). These and former results are discussed in terms of the mechanism of action of phenyalalanine and histidine ammonia lyases.